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PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VW1 experimental model PDB 4O9X
Sample PTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x TcdB2, 1 x TccC3) Sample Components TcdA1 TcdB2/TccC3
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument GATAN CRYOPLUNGE 3 Cryogen Name ETHANE Sample Vitrification Details blot 3 sec before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 89148 Reported Resolution (Å) 3.95 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (1VW1, 4O9X, 1VW1, 1VW1, 1VW1, 1VW1) Refinement Space REAL Refinement Protocol OTHER Refinement Target Model to Map FSC Overall B Value 68.03 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 2.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION EMAN2 IMAGE ACQUISITION EPU CTF CORRECTION SPHIRE MODEL FITTING UCSF Chimera 1.12 MODEL FITTING Rosetta INITIAL EULER ASSIGNMENT SPHIRE FINAL EULER ASSIGNMENT SPHIRE CLASSIFICATION SPHIRE RECONSTRUCTION SPHIRE MODEL REFINEMENT Rosetta MODEL REFINEMENT NAMD 2.12
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 205336